[ome-users] Question about Matlab Bio-Formats

[Melissa Linkert]

Hi Qi,

> Sorry for bother. I have a question about Matlab Bio-formats. Now, I use
> openThumbBytes() function to get the thumbnail image of WSI. But the size
> of it is fixed at 128.  This there any method to customized the thumbnail
> image size like (1000)?  I know, I could resize it when I get.But if I
> resize it from 128 to 1000, the image will become blur.
> 
> Secondly, sometime we want to get a re-scaled large part of WSI. for
> example, the whole WSI is 90000 x 90000, and we want [1:10000, 1:10000]
> area and save it to the size 500 x 500. I try to use bfgetPlane to extract
> 10000 x 10000 area from WSI and resize it by matlab. But the bfgetplane
> extraction part take a long time. Is there any quick method to do it? Thank
> you very much for your help.

If I understand correctly, you are working with files in the .ndpi
format.  The files should then contain the slide at several increasingly
smaller resolutions; you might try opening the resolution closest to the
size that you want, and resizing that.

Assuming 'reader' is the result of calling bfGetReader as mentioned
previously:

%%%%
% this is the number of resolutions, along with typically one or
% two extra barcode images (which are always the last images)
numberOfImages = reader.getSeriesCount();
% show the XY dimensions of each resolution
for i = 0 : numberOfImages - 1
  reader.setSeries(i);
  fprintf('resolution %s: width = %s, height = %s\n', i, reader.getSizeX(), reader.getSizeY())
end

% replace the number in the next line with the most appropriate
% resolution number from the above output
reader.setSeries(2);

imageWidth = reader.getSizeX();
imageHeight = reader.getSizeY();
% bfGetPlane can now be used as explained previously,
% but be careful to use the current value of imageWidth
% and imageHeight when calculating tile sizes
%%%%

That should also be faster than opening tiles from the full resolution
image and resizing them.  If that doesn't work though, please let us
know.

Regards,
-Melissa

On Thu, Apr 09, 2015 at 09:54:18AM -0400, Qi Gong wrote:
> Hello everyone,
> 
> Sorry for bother. I have a question about Matlab Bio-formats. Now, I use
> openThumbBytes() function to get the thumbnail image of WSI. But the size
> of it is fixed at 128.  This there any method to customized the thumbnail
> image size like (1000)?  I know, I could resize it when I get.But if I
> resize it from 128 to 1000, the image will become blur.
> 
> Secondly, sometime we want to get a re-scaled large part of WSI. for
> example, the whole WSI is 90000 x 90000, and we want [1:10000, 1:10000]
> area and save it to the size 500 x 500. I try to use bfgetPlane to extract
> 10000 x 10000 area from WSI and resize it by matlab. But the bfgetplane
> extraction part take a long time. Is there any quick method to do it? Thank
> you very much for your help.
> 
> Sincerely,
> Qi
> 
> 
> -- 
> mobile phone: 2024060862

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